Run DeXtrusion in Fiji thanks to Appose

DeXtrusion is a python module to detect cellular events like cell extrusions in epithelia movies.

You can install the plugin for the unliste update site Appose-Playground: in Fiji, go to Help>Update... then to Manage Update Sites in the window that opens. Click Add unliste update site, name it Appose-Playground and write its address https://sites.imagej.net/Appose-Playground.

Select the DeXtrusion_Appose-* .jar file to install only this plugin, or keep all proposed plugins. Press Apply changes and restart Fiji when it's done.

You can either run it on one opened image or on a batch of images. You can also record calling DeXtrusion and runs it in a macro.

To run it on one image, first open the image in Fiji, then starts the plugin in Plugins>DeXtrusion>Detect events

Select current image in Process

To run it on several images in batch mode, starts the plugin in Plugins>DeXtrusion>Detect events

Select several images (batch) in Process. When you will click on Ok, another window will pop-up to let you select the images to process.

First open the movie that you want to analyze. Go to Plugins>Dextrusion>Detect events

The program will first ask you to choose the parameters to run DeXtrusion on your movie. The parameters are:

• cell_diameter: typical cell diameter. This parameter is used to resize the movie if necessary, so that a cell is the same cell as the cells used in the training data (around 25 pixels).
• extrusion_duration: typical duration of a cell extrusion in the biological tissu, in frames. This is more or less the number of frames in which an extrusion event is visible. This parameter is used to resize temporally the movie is necessary, so that it fits the training data temporal resolution.

The plugin will run the detection with the default DeXtrusion models, notumAll that detect cell_death, cell_division events and cell_SOP probability.

You can change the used model, to select another one from DeXtrusion github or a customed model by going in Plugins>DeXtrusion>Set advanced parameters.